Our knowledge of eukaryotic transcription regulation has been mostly an extension from the prokaryotic studies. However, due to the very basic difference in how eukaryotes and prokaryotes organize their DNA, eukaryotic transcription regulation involves unique mechanisms which are not seen in the prokaryotic world. Eukaryotic DNA wraps around a class of non-specific DNA-binding proteins called histone to form nucleosomes. The strings of nucleosomes, called chromatin, would be packaged into several kinds of higher order structure, such as a 30 nm, or a 300 nm chromatin fiber. In the eukaryotic cell nucleus, transcription regulation involves dynamic reorganization of the higher order structure of chromatin. Due to the limitation of available technologies, the underlying mechanisms have not been very well understood.
The goal of our research is to understand mechanisms underlying the eukaryotic gene expression in the cell nucleus. We currently focus on a class of cis-regulatory elements called Chromatin Insulator or Boundary Element. This class of elements widely exists in eukaryotes from yeast to human and is proposed to organize genome into expression domains. Genes within an expression domain may have similar expression profiles because they are regulated by the same set of enhancers and silencers.
Accumulating evidence suggests that between two adjacent expression domains locates chromatin insulators which act as barriers to prevent cross boundary enhancer- or silencer-activities. We propose that the normal function of chromatin insulators, which is required for the establishment and maintenance of the expression domains, involves dynamically organizing the higher order structure of chromatin and recruiting necessary chromatin modification enzymes. We are using the gypsy insulator, which is one of the best studied chromatin insulators, as our model system to study the mechanisms underlying chromatin domain boundaries establishment and regulation. We are taking advantage of the very powerful Drosophila genetics combined with cell biology tools as our major approaches, In addition, we are developing genomic techniques to determine the distribution of chromatin insulators in a genome-wide scale.